interactionRemoval: interation-removal method
In mlDNA: Machine Learning-based Differential Network Analysis of Transcriptome Data
Description
Usage
Arguments
Value
Author(s)
References
Description
The interation-removal method is a gene selection approach based on the removal of interesected interactions in two networks, and has been applied to analyzed the rewiring of genetic interaction maps for identying yeast genes responsive to DNA damage (Bandyopadhyay, et al., 2010; Ideker and Krogan, 2012).
Usage
1
interactionRemoval( adjmat1, adjmat2, threshold1, threshold2 )
Arguments
adjmat1
adjacency matrix for condition1. The adjacency matrix can be generated using adjacencymatrix function in rsgcc package.
adjmat2
adjacency matrix for condition2.
threshold1
threshold used to mask low correlations in adjmat1.
threshold2
threshold used to mask low correlations in adjmat2.
Value
value
a matrix recording the specific degree of genes in the network constructed for condition 1.
Author(s)
Chuang Ma, Xiangfeng Wang
References
[1] Sourav Bandyopadhyay, Monika Mehta, Dwight Kuo, et al. Rewiring of genetic networks in response to DNA damage.Science, 2010, 330(6009): 1385-1389.
[2] Trey Ideker and Nevan J Krogan. Differential network biology. 2012, 8:565.
mlDNA documentation built on May 2, 2019, 2:15 p.m.
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Description Usage Arguments Value Author(s) References
Description
The interation-removal method is a gene selection approach based on the removal of interesected interactions in two networks, and has been applied to analyzed the rewiring of genetic interaction maps for identying yeast genes responsive to DNA damage (Bandyopadhyay, et al., 2010; Ideker and Krogan, 2012).
Usage
1 | interactionRemoval( adjmat1, adjmat2, threshold1, threshold2 )
|
Arguments
adjmat1 |
adjacency matrix for condition1. The adjacency matrix can be generated using adjacencymatrix function in rsgcc package. |
adjmat2 |
adjacency matrix for condition2. |
threshold1 |
threshold used to mask low correlations in adjmat1. |
threshold2 |
threshold used to mask low correlations in adjmat2. |
Value
value |
a matrix recording the specific degree of genes in the network constructed for condition 1. |
Author(s)
Chuang Ma, Xiangfeng Wang
References
[1] Sourav Bandyopadhyay, Monika Mehta, Dwight Kuo, et al. Rewiring of genetic networks in response to DNA damage.Science, 2010, 330(6009): 1385-1389.
[2] Trey Ideker and Nevan J Krogan. Differential network biology. 2012, 8:565.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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